In mammalian cells, RNA interference (RNAi) can be mediated by synthetic duplex RNAs, termed small interfering RNAs (siRNAs, by mediating the cleavage of completely complementary mRNA transcripts. MicroRNAs (miRNAs) are endogenous small RNAs that assist in translationally repressing mRNAs with regions of partial complementarity, but may also reduce transcript levels. Since miRNAs are thought to predominantly interact with the 3 untranslated regions (UTRs) of transcripts but little experimental data exists to support this, we sought to ask if mismatched siRNAs mimicking miRNAs affect cognate mRNA levels as a function of target site location. Our studies found that mismatched siRNAs targeting the 3 UTRs of two endogenous transcripts yield a greater reduction in mRNA levels than those targeting the coding region. Our findings demonstrated the importance of target site location within endogenous mRNAs for small RNAs associated with RNAi and these studies were published in FEBS Letters in 2006. To address if altered miRNA expression can contribute to the cancer process Dr. Caplen, (Section head, Gene Silencing Section (GSS), Genetics Branch), became involved in a study conducted by Dr. Curt Harriss group at CCR (Lab. of Human Carcinogenesis, (LHC), CCR, NCI) in collaboration with Dr. Carlo Croce, University of Iowa. Dr. Carlo Croce and others have previously shown that different types of cancer are associated with unique microRNA patterns, and that these patterns may be valuable in diagnosing and ascertaining prognosis. In this collaborative study (Yanaihara et al., 2006 Cancer Cell 9: 189-198), differential microRNA expression data from 104 pairs of primary lung cancers matched against adjacent normal tissue confirmed the deregulation of microRNAs in lung cancer reported in earlier papers, and uncovered a new microRNA marker associated with poor prognosis, hsa-miR-155. To further study the role of miRNA expression in cancer we have now established our own miRNA microarray based analysis within GSS using a commercial array platform (Ambion/ABI) and have begun extensive analysis of the miRNA expression breast cancer cell lines. This work has identified a number of miRNAs differential expressed in different breast cancer cell line. Follow up studies are focused on characterizing the putative targets of these differentially expressed miRNAs. Finally, we have examined a genomic region, human chromosome 8q24, commonly associated with Burkitts lymphoma and some solid tumors as a result of genetic rearrangements and/or deletions and amplifications for evidence of the presence of previously unidentified miRNAs. A number of studies have suggested that miRNAs may be clustered within known areas of genomic instability and we have recently reviewed this particular subject area with a special emphasis on the mouse genome (Huppi et al., Seminars in Cancer Biology). In collaboration with Drs. Natalia Volfovsky and Bob Stephens (ABCC, NCI-Fredrick/SAIC Frederick Inc. NCI, NIH) 12 possible miRNA precursor sequences were identified as mapping to within the human chr. 8q24 region, of which, 7 were experimentally verified. Further molecular and genetic studies investigating these novel miRNAs are on going in both human and mouse systems.